This study aims to determine the challenges of mainstreaming gender in the prevention of violent extremism in the North Eastern Kenya. The inclusion of women and girls and gender mainstreaming are often overlooked in efforts to counter violent extremism, despite being of core importance to many and to the human rights issues at stake in preventing violent extremism. Women in Kenya and north eastern in particular have for long been left out in the process of countering violent extremism; which has slowed down the progress to prevent future radicalization and extremism. The objectives of this research paper is to examine the Involvement of mainstreaming gender participation in Countering Violent Extremism, To determine the Inclusion of mainstreaming gender in the design, implementation, monitoring, and evaluation of Countering Violent Extremism efforts, To address adverse human rights impacts of Counter Violent Extremism and counter terrorism on women and girls .The study also attempts to answer questions such as why does gender matters in the prevention of violent extremism, the role of gender mainstreaming in prevention of violent extremism, the challenges of gender mainstreaming in prevention of violent extremism and the characteristics of violent extremists. This study adopted a case study research design. Data was collected from secondary sources. This involved reviewing material sources in the form of journals, books and reports. The collected data was analysed thematically by constructing themes that helped discuss the challenges of mainstreaming gender in the prevention of violent extremism in the North Eastern Kenya. Data was presented in a narrative form which was derived from evidence secondary sources that were used to support and illustrate themes. The conclusion and recommendation suggest that the government can successfully use some of the findings in the study to deal with the cases of the challenges of mainstreaming gender has to the prevention of violent extremism in the north eastern region of Kenya.